{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T13:18:03Z","timestamp":1776777483398,"version":"3.51.2"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,3]],"date-time":"2022-03-03T00:00:00Z","timestamp":1646265600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Generalitat Valenciana through PROMETEO grants program for excellence research groups [PROMETEO","award":["2016\/093"],"award-info":[{"award-number":["2016\/093"]}]},{"name":"Spanish MICINN","award":["PID2020-119537RB-I00"],"award-info":[{"award-number":["PID2020-119537RB-I00"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic datasets may combine data obtained in different batches where omics type and batch are often confounded. Moreover, systematic biases may be introduced without notice during data acquisition, which creates a hidden batch effect. Current methods fail to address batch effect correction in these cases.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this article, we introduce the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. The package includes a diversity of graphical outputs for model validation and assessment of the batch effect correction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>MultiBaC package is available on Bioconductor (https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/MultiBaC.html) and GitHub (https:\/\/github.com\/ConesaLab\/MultiBaC.git). The data underlying this article are available in Gene Expression Omnibus repository (accession numbers GSE11521, GSE1002, GSE56622 and GSE43747).<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac132","type":"journal-article","created":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T20:10:58Z","timestamp":1646165458000},"page":"2657-2658","source":"Crossref","is-referenced-by-count":17,"title":["MultiBaC: an R package to remove batch effects in multi-omic experiments"],"prefix":"10.1093","volume":"38","author":[{"given":"Manuel","family":"Ugidos","sequence":"first","affiliation":[{"name":"Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cient\u00edficas , Valencia 46010, Spain"},{"name":"Multivariate Statistical Engineering Group, Department of Applied Statistics, Operations Research and Quality, Universitat Polit\u00e8cnica de Val\u00e8ncia , Valencia 46022, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda Jos\u00e9","family":"Nueda","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Universidad de Alicante , Alicante 03690, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 M","family":"Prats-Montalb\u00e1n","sequence":"additional","affiliation":[{"name":"Multivariate Statistical Engineering Group, Department of Applied Statistics, Operations Research and Quality, Universitat Polit\u00e8cnica de Val\u00e8ncia , Valencia 46022, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alberto","family":"Ferrer","sequence":"additional","affiliation":[{"name":"Multivariate Statistical Engineering Group, Department of Applied Statistics, Operations Research and Quality, Universitat Polit\u00e8cnica de Val\u00e8ncia , Valencia 46022, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Conesa","sequence":"additional","affiliation":[{"name":"Institute for Integrative Systems Biology, Consejo Superior de Investigaciones Cient\u00edficas , Valencia 46980, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5346-1407","authenticated-orcid":false,"given":"Sonia","family":"Tarazona","sequence":"additional","affiliation":[{"name":"Multivariate Statistical Engineering Group, Department of Applied Statistics, Operations Research and Quality, Universitat Polit\u00e8cnica de Val\u00e8ncia , Valencia 46022, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,3]]},"reference":[{"key":"2023041402550013200_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1755-8794-5-23","article-title":"Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis","volume":"5","author":"Kupfer","year":"2012","journal-title":"BMC Med. 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